Hello Kathleen, The mritotal program is only run after our primary talairach alignment utility fails. Make sure your 'orig.mgz' looks 'good', that it, like the orig.mgz does in the sample subject 'bert': full head view with good orientation, and decent gm/wm contrast.
If it is ok, then a workaround is to use tkregister to manually align the image, such that mritotal is not run, and the rest of recon-all should run properly (hopefully). Let me know if this helps. -Zeke > On Feb 19, 2015, at 6:56 AM, Kathleen Durkin <durk...@nyspi.columbia.edu> > wrote: > > Hello. FreeSurfer newbie here. I have a data set of 14 subjects. I’ve > successfully run recon-all on 12 subjects but 2 are giving me the same error > message: > ERROR: mritotal failed, see transforms/talairach.log > > > > > Beneath that it says: > For more details, see the log file > /Users/kathleen/Documents/subjects/9304/scripts/recon-all.log > > > > > And the recon-all.log says, for mritotal: > mritotal -verbose -debug -clobber -modeldir > /Applications/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm > transforms/tmp.talairach.45457/src.mnc transforms/talairach.auto.xfm > Can't locate shellwords.pl in @INC (@INC contains: > /Applications/freesurfer/mni/bin/../lib/mni_autoreg > /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.10.0/darwin-thread-multi-2level > /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.10.0 > /Library/Perl/5.16/darwin-thread-multi-2level /Library/Perl/5.16 > /Network/Library/Perl/5.16/darwin-thread-multi-2level > /Network/Library/Perl/5.16 /Library/Perl/Updates/5.16.2 > /System/Library/Perl/5.16/darwin-thread-multi-2level > /System/Library/Perl/5.16 > /System/Library/Perl/Extras/5.16/darwin-thread-multi-2level > /System/Library/Perl/Extras/5.16 .) at > /Applications/freesurfer/mni/bin/mritotal line 460. > ERROR: mritotal failed, see transforms/talairach.log > Darwin Kathleens-MacBook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Wed > Dec 17 19:05:52 PST 2014; root:xnu-2422.115.10~1/RELEASE_X86_64 x86_64 > > recon-all -s 9304 exited with ERRORS at Thu Feb 19 09:49:28 EST 2015 > > > > > All of this is fairly opaque to me. Any ideas how to fix the problem? Thank > you in advance for your help. > > > Kathleen J. Durkin, M.S. > Director, Data Analysis and Training, MRI Research Program > New York State Psychiatric Institute > 1051 Riverside Drive > New York, NY 10032 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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